How to paint with the clone option in Texture Paint?
When the render is set to Cycles you can add two textures to the material and they should both show up as slots in texture paint.  Be sure to add a UV Map node for each texture and set the appropriate UV Map.

Enter Texture Paint mode and activate "Clone From Paint Slot".  

The texture that is being painted to should be selected in the section named "Available Paint Slots"

The texture that is being painted from should be selected in the section named "Source Clone Slot".

All the settings I used are shown in the following animation.



Update in response to a comment requesting more information.

Textures can be drag 'N dropped from the hard drive file system.  They can be added in as texture nodes by looking through the menu that is called up when the keyboard shortcut Shifts is used.  They can also be added by drag 'N dropping the image icon from the UV Image Editor.  



Using Blender Render you can add images to the texture slots.  I think the limit is 18 slots per material for BI.  I'm not sure if the BI node editor has the same limit, probably not.